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diff test-data/bw/test.xml @ 3:7342f467507b draft

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Uploaded v0.4 of JBrowse
author iuc
date Thu, 31 Dec 2015 13:58:43 -0500
parents
children ff11d442feed
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bw/test.xml	Thu Dec 31 13:58:43 2015 -0500
@@ -0,0 +1,132 @@
+<?xml version="1.0"?>
+<root>
+    <metadata>
+        <gencode>11</gencode>
+        <genomes>
+            <genome>test-data/merlin.fa</genome>
+        </genomes>
+    </metadata>
+    <tracks>
+        <track cat="Scaling" format="wiggle">
+            <files>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Auto Global"/>
+            </files>
+
+            <options>
+                <wiggle>
+                    <type>JBrowse/View/Track/Wiggle/XYPlot</type>
+                    <variance_band>true</variance_band>
+                    <autoscale>global</autoscale>
+                    <color_pos>__auto__</color_pos>
+                    <color_neg>__auto__</color_neg>
+                    <bicolor_pivot>zero</bicolor_pivot>
+                </wiggle>
+            </options>
+        </track>
+        <track cat="Scaling" format="wiggle">
+            <files>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Auto Local"/>
+            </files>
+
+            <options>
+                <wiggle>
+                    <type>JBrowse/View/Track/Wiggle/XYPlot</type>
+                    <variance_band>true</variance_band>
+                    <autoscale>local</autoscale>
+                    <color_pos>__auto__</color_pos>
+                    <color_neg>__auto__</color_neg>
+                    <bicolor_pivot>zero</bicolor_pivot>
+                </wiggle>
+            </options>
+        </track>
+        <track cat="Scaling" format="wiggle">
+            <files>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Manual"/>
+            </files>
+
+            <options>
+                <wiggle>
+                    <type>JBrowse/View/Track/Wiggle/XYPlot</type>
+                    <variance_band>false</variance_band>
+                    <autoscale>fixed</autoscale>
+                    <min>20</min>
+                    <max>60</max>
+                    <color_pos>__auto__</color_pos>
+                    <color_neg>__auto__</color_neg>
+                    <bicolor_pivot>zero</bicolor_pivot>
+                </wiggle>
+            </options>
+        </track>
+
+
+        <track cat="Colouring" format="wiggle">
+            <files>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Auto A"/>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Auto B"/>
+            </files>
+
+            <options>
+                <wiggle>
+                    <type>JBrowse/View/Track/Wiggle/XYPlot</type>
+                    <variance_band>false</variance_band>
+                    <autoscale>local</autoscale>
+
+                    <color_pos>__auto__</color_pos>
+                    <color_neg>__auto__</color_neg>
+                    <bicolor_pivot>mean</bicolor_pivot>
+                </wiggle>
+            </options>
+        </track>
+        <track cat="Colouring" format="wiggle">
+            <files>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Manual"/>
+            </files>
+
+            <options>
+                <wiggle>
+                    <type>JBrowse/View/Track/Wiggle/XYPlot</type>
+                    <variance_band>false</variance_band>
+                    <autoscale>local</autoscale>
+
+                    <color_pos>#0000ff</color_pos>
+                    <color_neg>#ff0000</color_neg>
+                    <bicolor_pivot>mean</bicolor_pivot>
+                </wiggle>
+            </options>
+        </track>
+        <track cat="Colouring" format="wiggle">
+            <files>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Manual - Inverted"/>
+            </files>
+
+            <options>
+                <wiggle>
+                    <type>JBrowse/View/Track/Wiggle/XYPlot</type>
+                    <variance_band>false</variance_band>
+                    <autoscale>local</autoscale>
+
+                    <color_pos>#ff0000</color_pos>
+                    <color_neg>#0000ff</color_neg>
+                    <bicolor_pivot>mean</bicolor_pivot>
+                </wiggle>
+            </options>
+        </track>
+        <track cat="Colouring" format="wiggle">
+            <files>
+                <trackFile path="test-data/bw/data.bw" ext="bigwig" label="Nonstandard Pivot"/>
+            </files>
+
+            <options>
+                <wiggle>
+                    <type>JBrowse/View/Track/Wiggle/XYPlot</type>
+                    <variance_band>false</variance_band>
+                    <autoscale>local</autoscale>
+
+                    <color_pos>#0000ff</color_pos>
+                    <color_neg>#ff0000</color_neg>
+                    <bicolor_pivot>100</bicolor_pivot>
+                </wiggle>
+            </options>
+        </track>
+    </tracks>
+</root>